Manafort's guilty plea relates to money earned from consulting work on behalf of pro-Russia politicians in Ukraine and predates his time with the Trump campaign. However, Manafort has agreed to cooperate "in any and all matters as to which the government deems the cooperation relevant."
The special counsel is investigating Russia's interference in the 2016 election, as well as possible conspiracy between members of the Trump campaign and the Kremlin. Mueller is also reportedly looking into whether the president obstructed justice in an effort to influence the Russia probe.
Manafort attended a controversial meeting at Trump Tower during the campaign. Also in attendance were Trump's son Donald Trump Jr. and son-in-law, Jared Kushner, along with a Russian lawyer who was offering dirt about Democratic presidential nominee Hillary Clinton.
"If the president were to pardon him now and allow him to walk free tomorrow, Bob Mueller already knows the answers to those questions, and he can still compel him to testify with a grand jury subpoena. He can compel him to testify at trial," Miller explained.
And if Manafort gave answers that contradicted what he already told prosecutors under oath, he could be charged with perjury, he added.
Famed defense attorney Alan Dershowitz, author of "The Case Against Impeaching Trump," told MSNBC on Friday that Manafort was probably hoping for a pardon but agreed now it is "too little, too late."
"There will be no pardon. It would backfire at this point because, number one, if he's given a pardon, then he can't take the Fifth Amendment," he said. "He would have to testify anyway. He could be called in front of a grand jury. So the pardon is off the table."
Dershowitz said it remains to be seen whether Manafort's plea deal will help prosecutors.
The White House and Trump's attorneys responded swiftly to the deal.
"This had absolutely nothing to do with the President or his victorious 2016 Presidential campaign," White House press secretary Sarah Huckabee Sanders said on Friday. "It is totally unrelated."
Rudy Giuliani, Trump's attorney for the Russia probe, said: "Once again an investigation has concluded with a plea having nothing to do with President Trump or the Trump campaign."
"The reason: the President did nothing wrong and Paul Manafort will tell the truth," Giuliani said.
However, minutes after Giuliani's statement was released, another Trump lawyer, Jay Sekulow, sent a "corrected statement" that said the same thing but omitted the words "and Paul Manafort will tell the truth."
— CNBC's Dan Mangan contributed to this report.